Detection of Viral Proteins in Human Cells Lines by Xeno-Proteomics: Elimination of the Last Valid Excuse for Not Testing Every Cellular Proteome Dataset for Viral Proteins

Chernobrovkin, Alexey L.; Zubarev, Roman A.

The procedure can also be applied to already acquired data. A recent editorial in Nature Methods urges researchers to reprocess existing proteomics raw data ''with new questions in mind…'' [27] . Here we followed this advice and used published proteomics data. First, proof of principle is obtained by discovering expected viruses in cell lines known to be producing viral proteins (both cell line established by viral transfection and cell line known to be contaminated by virus). As a control, we analyzed proteomes of 58 NCI-obtained cell lines from the NCI-60 panel. This panel has previously been screened for envelope viral proteins and gene sequences related to xenotropic murine leukemia viruses (X-MLVs) [28] and only one cell line, EKVX, has been found infected by xenotropic murine leukemia virus. Finally, we applied the three-step procedure to other cell line proteomes analyzed by a reputable group [18] and discovered unexpected viral contamination in at least one of the reported 11 lines.